Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000129.1 Kokia drynarioides strain JFW-HI SEQ_110775, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 83224
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1525 original size:41 final size:41
Alignment explanation
Indices: 1478--1580 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
1468 ACCCTTAACT
*
1478 CTTTGACCTTTAGCGGTGCTTGCACAAAAGTGCCGCTATTA
1 CTTTGACCTTTAGCGGTGCTTGCACAAAAGCGCCGCTATTA
* * *
1519 CTTTGACCTTTAGCGGCGCTTGCACAAAAGCGTCGCTATTG
1 CTTTGACCTTTAGCGGTGCTTGCACAAAAGCGCCGCTATTA
* *
1560 CTCTGACCTTTAGAGGTGCTT
1 CTTTGACCTTTAGCGGTGCTT
1581 TCCCCTAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.32
Consensus pattern (41 bp):
CTTTGACCTTTAGCGGTGCTTGCACAAAAGCGCCGCTATTA
Found at i:7179 original size:21 final size:19
Alignment explanation
Indices: 7133--7181 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
7123 GTGTAGAATT
7133 AGTTTAGTTGTTGTAAATA
1 AGTTTAGTTGTTGTAAATA
*
7152 TGTTTAGTTGATTAG-AAAGTA
1 AGTTTAGTTG-TT-GTAAA-TA
7173 AGTTTAGTT
1 AGTTTAGTT
7182 TAGTAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 9 0.36
20 5 0.20
21 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (19 bp):
AGTTTAGTTGTTGTAAATA
Found at i:8456 original size:295 final size:295
Alignment explanation
Indices: 7906--8499 Score: 996
Period size: 295 Copynumber: 2.0 Consensus size: 295
7896 ACCCATATCA
* *
7906 ATTGAGTTAAAATTCAATCAGCAATACTTGTCAAGGAATTTCCAAATTAAAATTATGTGGGGAAT
1 ATTGAGTTAAAATTCAATCAACAATACTTGTCAAGAAATTTCCAAATTAAAATTATGTGGGGAAT
* * *
7971 GGAAGGAAAGACAAAAACAAGGCTATATATTTTCTGTATACCTAACCTAAAAAAGGCCTAGATAA
66 GGAAGGAAAGACAAAAAAAAAGCTATATATTTTCTATATACCTAACCTAAAAAAGGCCTAGATAA
* **
8036 TCAGCCTACATCCACAGTGAAATTGAACTAAAGGAGGCCTTTTAATTCCTTAGATTGGGTTGGAA
131 TCAGCCTACATCCACAATGAAATTGAACTAAAGGAGGCCTTTTAATTCCTTAGATTGGACTGGAA
8101 TGGATGATGACTAAAATCAACTCATTGCATTTTTTTTCTTTACAATAACTTTGAGTCCCTGATAG
196 TGGATGATGACTAAAATCAACTCATTGCATTTTTTTTCTTTACAATAACTTTGAGTCCCTGATAG
8166 CTTACAACTCAAATAACAAATTAATGTAAAAATTC
261 CTTACAACTCAAATAACAAATTAATGTAAAAATTC
8201 ATTGAGTTAAAATTCAATCAACAATACTTGTCAAGAAATTTCCAAATTAAAATTATGT-GGGAAT
1 ATTGAGTTAAAATTCAATCAACAATACTTGTCAAGAAATTTCCAAATTAAAATTATGTGGGGAAT
* * *
8265 GGAAGGAAAGACAAAAAAAAAAGCTATATATTTTCTATATATCTGACCTAAAAGAGGCCTAGATA
66 GGAAGGAAAGAC-AAAAAAAAAGCTATATATTTTCTATATACCTAACCTAAAAAAGGCCTAGATA
*
8330 ATCAGCCTACA-CTCATAATGAAATTGAACTAAAGGAGGCCTTTTAATTCCTTAGATTGGACTGG
130 ATCAGCCTACATC-CACAATGAAATTGAACTAAAGGAGGCCTTTTAATTCCTTAGATTGGACTGG
*
8394 AATGGAATGATGACTAAAATCAACTCTTTGCATTTTTTTTCTTTACAATAACTTTG-GTCCCTGA
194 AATGG-ATGATGACTAAAATCAACTCATTGCATTTTTTTTCTTTACAATAACTTTGAGTCCCTGA
* * *
8458 TAGCTTACAACTCAAATAATAAATTAGTGTAAATATTC
258 TAGCTTACAACTCAAATAACAAATTAATGTAAAAATTC
8496 ATTG
1 ATTG
8500 GATCCCTGAT
Statistics
Matches: 280, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
294 19 0.07
295 212 0.76
296 49 0.17
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (295 bp):
ATTGAGTTAAAATTCAATCAACAATACTTGTCAAGAAATTTCCAAATTAAAATTATGTGGGGAAT
GGAAGGAAAGACAAAAAAAAAGCTATATATTTTCTATATACCTAACCTAAAAAAGGCCTAGATAA
TCAGCCTACATCCACAATGAAATTGAACTAAAGGAGGCCTTTTAATTCCTTAGATTGGACTGGAA
TGGATGATGACTAAAATCAACTCATTGCATTTTTTTTCTTTACAATAACTTTGAGTCCCTGATAG
CTTACAACTCAAATAACAAATTAATGTAAAAATTC
Found at i:15854 original size:24 final size:25
Alignment explanation
Indices: 15794--15854 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
15784 CTAATTAAAA
** *
15794 TTAATTAAAACCATTTTTTAGATGT
1 TTAATTAAAATTACTTTTTAGATGT
*
15819 TTAATTATAATTACTTTTTAGATGT
1 TTAATTAAAATTACTTTTTAGATGT
15844 TTAA-TAAAATT
1 TTAATTAAAATT
15855 TTAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (25 bp):
TTAATTAAAATTACTTTTTAGATGT
Found at i:22100 original size:29 final size:30
Alignment explanation
Indices: 22067--22160 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
22057 ACAAGGAAAA
*
22067 AGGGGTCAAA-ATGAAATTTTGGAAAGTTT
1 AGGGGCCAAATATGAAATTTTGGAAAGTTT
* *
22096 AGGGGCCAAATTTGAATTTTTGGAAAGTTT
1 AGGGGCCAAATATGAAATTTTGGAAAGTTT
** * *
22126 ACAGGCCAAAT-TCAAATTTTTGAAAAGTTT
1 AGGGGCCAAATATGAAA-TTTTGGAAAGTTT
22156 GAGGG
1 -AGGG
22161 TAAAAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 12 0.23
30 38 0.73
31 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (30 bp):
AGGGGCCAAATATGAAATTTTGGAAAGTTT
Found at i:22119 original size:30 final size:30
Alignment explanation
Indices: 22078--22160 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
22068 GGGGTCAAAA
*
22078 TGAAATTTTGGAAAGTTTAGGGGCCAAATT
1 TGAATTTTTGGAAAGTTTAGGGGCCAAATT
**
22108 TGAATTTTTGGAAAGTTTACAGGCCAAATT
1 TGAATTTTTGGAAAGTTTAGGGGCCAAATT
** *
22138 CAAATTTTTGAAAAGTTTGAGGG
1 TGAATTTTTGGAAAGTTT-AGGG
22161 TAAAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 42 0.95
31 2 0.05
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (30 bp):
TGAATTTTTGGAAAGTTTAGGGGCCAAATT
Found at i:22222 original size:30 final size:30
Alignment explanation
Indices: 22089--22224 Score: 82
Period size: 30 Copynumber: 4.6 Consensus size: 30
22079 GAAATTTTGG
* * **
22089 AAAGTTTAGG-GGCCAAATTTGAATTTTTGG
1 AAAGTTT-GGAGGTCAAATTTAAATTTTTAA
** * * *
22119 AAAGTTTACAGGCCAAATTCAAATTTTTGA
1 AAAGTTTGGAGGTCAAATTTAAATTTTTAA
*** *
22149 AAAGTTT-GAGGGT-AAAAAAAAATTTTTAG
1 AAAGTTTGGA-GGTCAAATTTAAATTTTTAA
* *
22178 AAAG-TTCGAGGGTCAAATTTGAATTTTTAA
1 AAAGTTTGGA-GGTCAAATTTAAATTTTTAA
22208 AAAGTTTGGAGGTCAAA
1 AAAGTTTGGAGGTCAAA
22225 ATATTATTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.02
29 22 0.27
30 55 0.66
31 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (30 bp):
AAAGTTTGGAGGTCAAATTTAAATTTTTAA
Found at i:31895 original size:31 final size:31
Alignment explanation
Indices: 31860--31918 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
31850 ATTTAAATGT
*
31860 ATATAATTAAA-TCAAAATGAAAGTTTTACAA
1 ATATAATTAAACT-AAAATCAAAGTTTTACAA
* *
31891 ATATATTTAAACTACAATCAAAGTTTTA
1 ATATAATTAAACTAAAATCAAAGTTTTA
31919 AGTGTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (31 bp):
ATATAATTAAACTAAAATCAAAGTTTTACAA
Found at i:32695 original size:57 final size:57
Alignment explanation
Indices: 32599--32737 Score: 217
Period size: 57 Copynumber: 2.5 Consensus size: 57
32589 GTGTCGGCTC
* * *
32599 TTTATCAGATAAAAAAATA-TTTTTTTGATGTCGCTCATGCCATGGCCGACACCACT
1 TTTATCTGATAAAAAAATATTTTTTTTGATGTCGCCCATGCCATGACCGACACCACT
* *
32655 TTTATCTGATAAAAAAATATTTTTTTTGATGTCGCCCATGCCATGATCGATACCACT
1 TTTATCTGATAAAAAAATATTTTTTTTGATGTCGCCCATGCCATGACCGACACCACT
*
32712 TTTATTTGATAAAAAAATATTTTTTT
1 TTTATCTGATAAAAAAATATTTTTTT
32738 GGGGTTGTGC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 18 0.24
57 58 0.76
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.40
Consensus pattern (57 bp):
TTTATCTGATAAAAAAATATTTTTTTTGATGTCGCCCATGCCATGACCGACACCACT
Found at i:43479 original size:17 final size:18
Alignment explanation
Indices: 43453--43496 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
43443 CTCCCCTCTC
43453 TCATCATCACCATCACCA
1 TCATCATCACCATCACCA
* *
43471 TCA-CATCACCGTTACCA
1 TCATCATCACCATCACCA
43488 TCATCATCA
1 TCATCATCA
43497 AAAGCTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (18 bp):
TCATCATCACCATCACCA
Found at i:48060 original size:3 final size:3
Alignment explanation
Indices: 48052--48079 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48042 ACCTTCTCTT
48052 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48080 ATCTCCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48368 original size:18 final size:18
Alignment explanation
Indices: 48353--48386 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48343 ATTTTTATAT
48353 ATTTT-TAAAATTTTATG
1 ATTTTATAAAATTTTATG
*
48370 ATTTTATAATATTTTAT
1 ATTTTATAAAATTTTAT
48387 CATTATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTATAAAATTTTATG
Found at i:48498 original size:19 final size:19
Alignment explanation
Indices: 48476--48522 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
48466 TATTTATCAG
48476 ATTTTATGATT-TTTTTATA
1 ATTTTAT-ATTATTTTTATA
48495 ATTTT-TATTAGTTTTTATA
1 ATTTTATATTA-TTTTTATA
48514 ATATTTATA
1 AT-TTTATA
48523 AGTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 15 0.62
20 3 0.12
21 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (19 bp):
ATTTTATATTATTTTTATA
Found at i:48520 original size:9 final size:9
Alignment explanation
Indices: 48343--48599 Score: 102
Period size: 10 Copynumber: 27.8 Consensus size: 9
48333 CTATAAATGG
48343 ATTTTTATA
1 ATTTTTATA
48352 TATTTTTA-A
1 -ATTTTTATA
* *
48361 AATTTTATG
1 ATTTTTATA
48370 A-TTTTATA
1 ATTTTTATA
*
48378 ATATTTTATC
1 AT-TTTTATA
* *
48388 ATTATTAGA
1 ATTTTTATA
48397 ACTTTTTATA
1 A-TTTTTATA
*
48407 AGTTTTTATC
1 A-TTTTTATA
*
48417 CTGTTTTAATA
1 AT-TTTT-ATA
*
48428 AGTTTTATA
1 ATTTTTATA
*
48437 ATTATTGATA
1 ATT-TTTATA
48447 ATTTTT-TA
1 ATTTTTATA
48455 GAGTTTTTA-A
1 -A-TTTTTATA
*
48465 ATATTTATCA
1 ATTTTTAT-A
48475 GA-TTTTATGA
1 -ATTTTTAT-A
*
48485 TTTTTTTATA
1 -ATTTTTATA
48495 ATTTTTATTA
1 ATTTTTA-TA
*
48505 GTTTTTATA
1 ATTTTTATA
*
48514 ATATTTATA
1 ATTTTTATA
*
48523 AGTTATTAT-
1 A-TTTTTATA
*
48532 -TTTTT-TT
1 ATTTTTATA
48539 ATTTTT-TA
1 ATTTTTATA
* *
48547 GTTTATATA
1 ATTTTTATA
*
48556 ATATTTTATT
1 AT-TTTTATA
*
48566 A-TTTTATT
1 ATTTTTATA
48574 ATTTTTATTA
1 ATTTTTA-TA
* *
48584 TTTTTTACA
1 ATTTTTATA
48593 ATTTTTA
1 ATTTTTA
48600 ATATGAAAAA
Statistics
Matches: 185, Mismatches: 40, Indels: 45
0.69 0.15 0.17
Matches are distributed among these distances:
6 1 0.01
7 4 0.02
8 38 0.21
9 48 0.26
10 85 0.46
11 9 0.05
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:48526 original size:19 final size:19
Alignment explanation
Indices: 48487--48531 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
48477 TTTTATGATT
* *
48487 TTTTTATAATTTTTATTAG
1 TTTTTATAATATTTATAAG
48506 TTTTTATAATATTTATAAG
1 TTTTTATAATATTTATAAG
*
48525 TTATTAT
1 TTTTTAT
48532 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTATAATATTTATAAG
Found at i:48573 original size:44 final size:42
Alignment explanation
Indices: 48476--48590 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 42
48466 TATTTATCAG
* *
48476 ATTTTATGATTTTTTTATAATTTTTATTAGTTTTTATAATATTTAT
1 ATTTTATTATTTTTTT-T-A-TTTT-TTAGTTTATATAATATTTAT
**
48522 AAGTTATTATTTTTTTTATTTTTTAGTTTATATAATATTTTATT
1 ATTTTATTATTTTTTTTATTTTTTAGTTTATATAATA-TTTA-T
*
48566 ATTTTATTATTTTTATTATTTTTTA
1 ATTTTATTATTTTTTTTATTTTTTA
48591 CAATTTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 14 0.23
43 8 0.13
44 24 0.40
45 1 0.02
46 13 0.22
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (42 bp):
ATTTTATTATTTTTTTTATTTTTTAGTTTATATAATATTTAT
Found at i:54559 original size:5 final size:5
Alignment explanation
Indices: 54545--54609 Score: 85
Period size: 5 Copynumber: 13.0 Consensus size: 5
54535 TAAATAACCA
* * * * *
54545 CCCTT CCCTT TCCTT TCCTT TCCTT TCCTT TCCTT CCCTT CCCTT CCCTT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT
54595 CCCTT CCCTT CCCTT
1 CCCTT CCCTT CCCTT
54610 TCTTCCAACC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 58 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (5 bp):
CCCTT
Found at i:64121 original size:53 final size:54
Alignment explanation
Indices: 64041--64179 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 54
64031 GTGTTAGGAT
* *
64041 ATTATTATGCGATATTATCTTTTAGCAATTTAATTCCTAATGTGATATTAT-AG-
1 ATTATTATGAGATATTATC-TTTAGCAATTTAATTCCTAATGGGATATTATAAGA
* * * *
64094 ATTATTATGAAATATTATCTCTTAGCAATTTGATTTCTAATGGGATATTGTAAGA
1 ATTATTATGAGATATTATCT-TTAGCAATTTAATTCCTAATGGGATATTATAAGA
*
64149 TATTATTATGAGATATTATCTTTAGTAATTT
1 -ATTATTATGAGATATTATCTTTAGCAATTT
64180 GATTTCTATG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
52 1 0.01
53 43 0.58
54 2 0.03
55 9 0.12
56 19 0.26
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (54 bp):
ATTATTATGAGATATTATCTTTAGCAATTTAATTCCTAATGGGATATTATAAGA
Found at i:66734 original size:62 final size:62
Alignment explanation
Indices: 66637--66753 Score: 225
Period size: 62 Copynumber: 1.9 Consensus size: 62
66627 GATGCTAGGC
66637 TGGGGTGCCAACTATTGCATTGGGCCAGCGTCGTGGTATTGGATTGTGAGGCTACGACTTGA
1 TGGGGTGCCAACTATTGCATTGGGCCAGCGTCGTGGTATTGGATTGTGAGGCTACGACTTGA
*
66699 TGGGGTGCCAACTATTGCATTGGGCCAGCTTCGTGGTATTGGATTGTGAGGCTAC
1 TGGGGTGCCAACTATTGCATTGGGCCAGCGTCGTGGTATTGGATTGTGAGGCTAC
66754 AACCTGATCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (62 bp):
TGGGGTGCCAACTATTGCATTGGGCCAGCGTCGTGGTATTGGATTGTGAGGCTACGACTTGA
Found at i:68115 original size:23 final size:24
Alignment explanation
Indices: 68089--68135 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
68079 TTGACAAATG
* *
68089 AAGAAGAACAACAA-ACCAAAAAA
1 AAGAAAAACAAAAATACCAAAAAA
*
68112 AAGAAAAAGAAAAATACCAAAAAA
1 AAGAAAAACAAAAATACCAAAAAA
68136 TTACTTATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.02
Consensus pattern (24 bp):
AAGAAAAACAAAAATACCAAAAAA
Found at i:68316 original size:26 final size:26
Alignment explanation
Indices: 68287--68345 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
68277 AATTTTTTCG
68287 AATCGAGTCGAGTAAAATGAAATTCA
1 AATCGAGTCGAGTAAAATGAAATTCA
*
68313 AATCGAGTCGAGTGAAATGAAATTCA
1 AATCGAGTCGAGTAAAATGAAATTCA
68339 AATCGAG
1 AATCGAG
68346 ACAAATCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (26 bp):
AATCGAGTCGAGTAAAATGAAATTCA
Found at i:69065 original size:30 final size:30
Alignment explanation
Indices: 69029--69093 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
69019 CATAACACCT
69029 AGACCTGATCATGGGTCGGGCCATTCGATC
1 AGACCTGATCATGGGTCGGGCCATTCGATC
69059 AGACCTGATCATGGGTCGGGCCATTCGATC
1 AGACCTGATCATGGGTCGGGCCATTCGATC
69089 AGACC
1 AGACC
69094 CGAATGTCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.22
Consensus pattern (30 bp):
AGACCTGATCATGGGTCGGGCCATTCGATC
Found at i:69347 original size:19 final size:20
Alignment explanation
Indices: 69274--69360 Score: 85
Period size: 19 Copynumber: 4.5 Consensus size: 20
69264 AATTATATTG
69274 TTGTTTTGGTGCTTTTTTTA
1 TTGTTTTGGTGCTTTTTTTA
* * *
69294 CTGTTTTGGTTGTTGTTTTTTG
1 TTGTTTTGG-TGCT-TTTTTTA
*
69316 TTGTTTT--T--ATTTTTTA
1 TTGTTTTGGTGCTTTTTTTA
69332 TTGTTTTGGTG-TTTTTTTA
1 TTGTTTTGGTGCTTTTTTTA
69351 TTGTTTTGGT
1 TTGTTTTGGT
69361 TGTTATTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
16 13 0.24
18 1 0.02
19 18 0.33
20 8 0.15
21 3 0.05
22 12 0.22
ACGTcount: A:0.05, C:0.02, G:0.21, T:0.72
Consensus pattern (20 bp):
TTGTTTTGGTGCTTTTTTTA
Found at i:69374 original size:19 final size:19
Alignment explanation
Indices: 69331--69390 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 19
69321 TTTATTTTTT
* *
69331 ATTGTTTTGGTGTTTTTTT
1 ATTGTTTTGGTGTTATTTC
69350 ATTGTTTTGGTTGTTATTTC
1 ATTGTTTTGG-TGTTATTTC
*
69370 ATGTTGTTTTCGCTGTTATTT
1 A--TTGTTTT-GGTGTTATTT
69391 TTGTTGCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 8 0.24
22 15 0.44
23 1 0.03
ACGTcount: A:0.08, C:0.05, G:0.20, T:0.67
Consensus pattern (19 bp):
ATTGTTTTGGTGTTATTTC
Found at i:69436 original size:24 final size:24
Alignment explanation
Indices: 69409--69479 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 24
69399 ATTTTTTTTG
*
69409 TTTTTAATGTTG-TTT-GCTGTTA
1 TTTTTTATGTTGTTTTGGCTGTTA
*
69431 TTTTTTATGTTGTTTTGGTTGTTA
1 TTTTTTATGTTGTTTTGGCTGTTA
*
69455 --TTTT-TGTTGTTTT-GATGTTA
1 TTTTTTATGTTGTTTTGGCTGTTA
69475 TTTTT
1 TTTTT
69480 ATGCGATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.14
21 9 0.21
22 18 0.43
23 3 0.07
24 6 0.14
ACGTcount: A:0.10, C:0.01, G:0.18, T:0.70
Consensus pattern (24 bp):
TTTTTTATGTTGTTTTGGCTGTTA
Found at i:69453 original size:43 final size:43
Alignment explanation
Indices: 69343--69479 Score: 152
Period size: 43 Copynumber: 3.1 Consensus size: 43
69333 TGTTTTGGTG
*
69343 TTTTTTTATTGTTTTGGTTGTTATTTCATGTTGTTTTCGCTGTTA
1 TTTTTTTGTTGTTTTGGTTGTTATTT-ATGTTGTTTT-GCTGTTA
* * **
69388 TTTTTGTTGCTATTTTTTTTGTT-TTTAATGTTG-TTTGCTGTTA
1 TTTTT-TTGTTGTTTTGGTTGTTATTT-ATGTTGTTTTGCTGTTA
* *
69431 TTTTTTATGTTGTTTTGGTTGTTATTTTTGTTGTTTTGATGTTA
1 TTTTTT-TGTTGTTTTGGTTGTTATTTATGTTGTTTTGCTGTTA
69475 TTTTT
1 TTTTT
69480 ATGCGATTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
42 1 0.01
43 29 0.38
44 20 0.26
45 14 0.18
46 12 0.16
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.70
Consensus pattern (43 bp):
TTTTTTTGTTGTTTTGGTTGTTATTTATGTTGTTTTGCTGTTA
Found at i:69625 original size:16 final size:16
Alignment explanation
Indices: 69594--69624 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
69584 TAATATAAAA
69594 AAATTTAATTTATTTT
1 AAATTTAATTTATTTT
69610 AAATTT-ATTTATTTT
1 AAATTTAATTTATTTT
69625 TTTAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AAATTTAATTTATTTT
Done.